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Literature summary for 2.3.1.304 extracted from
- Polyhydroxyalkanoate (PHA) synthase genes and PHA-associated gene clusters in Pseudomonas spp. and Janthinobacterium spp. isolated from Antarctica (2020), J. Biotechnol., 313, 18-28 .
Cloned(Commentary)
| Cloned (Comment) | Organism |
|---|---|
| cloning from the PHAC cluster, DNA and amino acid sequence determination and analysis, phylogenetic analysis, genotyping | Pseudomonas sp. UMAB-08 |
| cloning from the PHAC cluster, DNA and amino acid sequence determination and analysis, phylogenetic analysis, genotyping | Pseudomonas sp. UMAB-40 |
| cloning from the PHAC cluster, DNA and amino acid sequence determination and analysis, phylogenetic analysis, genotyping, functional recombinant heterologous expression in the PHA-negative mutant of Cupriavidus necator PHB-4 | Janthinobacterium sp. UMAB-56 |
| cloning from the PHAC cluster, DNA and amino acid sequence determination and analysis, phylogenetic analysis, genotyping, functional recombinant heterologous expression in the PHA-negative mutant of Cupriavidus necator PHB-4 | Janthinobacterium sp. UMAB-60 |
| cloning from the PHAC cluster, DNA and amino acid sequence determination and analysis, phylogenetic analysis, genotyping, recombinant expression in the PHA-negative mutant of Cupriavidus necator PHB-4 shows that the enzyme is not functional | Janthinobacterium sp. UMAB-58 |
| cloning from the PHAC cluster, DNA and amino acid sequence determination and analysis, phylogenetic analysis, genotyping, recombinant heterologous expression in the PHA-negative mutant of Cupriavidus necator PHB-4. PHB-4/pBBR1-ProCnJ60 accumulates 18.7% of wild-type polyhydroxybutyrate | Janthinobacterium sp. UMAB-60 |
Localization
| Localization | Comment | Organism | GeneOntology No. | Textmining |
|---|---|---|---|---|
| cytoplasm | - |
Janthinobacterium sp. UMAB-56 | 5737 | - |
| cytoplasm | - |
Janthinobacterium sp. UMAB-60 | 5737 | - |
| cytoplasm | - |
Pseudomonas sp. UMAB-08 | 5737 | - |
| cytoplasm | - |
Pseudomonas sp. UMAB-40 | 5737 | - |
Natural Substrates/ Products (Substrates)
| Natural Substrates | Organism | Comment (Nat. Sub.) | Natural Products | Comment (Nat. Pro.) | Rev. | Reac. |
|---|---|---|---|---|---|---|
| (R)-3-hydroxybutanoyl-CoA + [(R)-3-hydroxybutanoate]n | Pseudomonas sp. UMAB-08 | - |
[(R)-3-hydroxybutanoate](n+1) + CoA | - |
? |  |
| (R)-3-hydroxybutanoyl-CoA + [(R)-3-hydroxybutanoate]n | Pseudomonas sp. UMAB-40 | - |
[(R)-3-hydroxybutanoate](n+1) + CoA | - |
? | |
Organism
| Organism | UniProt | Comment | Textmining |
|---|---|---|---|
| Janthinobacterium sp. UMAB-56 | - |
isolated from Antarctica | - |
| Janthinobacterium sp. UMAB-58 | - |
isolated from Antarctica | - |
| Janthinobacterium sp. UMAB-60 | - |
isolated from Antarctica | - |
| Pseudomonas sp. UMAB-08 | - |
isolated from Antarctica | - |
| Pseudomonas sp. UMAB-40 | - |
isolated from Antarctica | - |
Substrates and Products (Substrate)
| Substrates | Comment Substrates | Organism | Products | Comment (Products) | Rev. | Reac. |
|---|---|---|---|---|---|---|
| (R)-3-hydroxybutanoyl-CoA + [(R)-3-hydroxybutanoate]n | - |
Pseudomonas sp. UMAB-08 | [(R)-3-hydroxybutanoate](n+1) + CoA | - |
? | |
| (R)-3-hydroxybutanoyl-CoA + [(R)-3-hydroxybutanoate]n | - |
Pseudomonas sp. UMAB-40 | [(R)-3-hydroxybutanoate](n+1) + CoA | - |
? | |
| additional information | PHA biosynthesis and in vitro PhaC enzymatic assay results show that the uncharacterized putative PHA synthase from Janthinobacterium sp. UMAB-58 is not funtional | Janthinobacterium sp. UMAB-58 | ? | - |
- |
|
| additional information | PHA biosynthesis and in vitro PhaC enzymatic assay results show that the uncharacterized putative PHA synthase from Janthinobacterium sp. UMAB-60 is funtional | Janthinobacterium sp. UMAB-60 | ? | - |
- |
|
Synonyms
| Synonyms | Comment | Organism |
|---|---|---|
| class I PHA synthase | - |
Janthinobacterium sp. UMAB-56 |
| class I PHA synthase | - |
Janthinobacterium sp. UMAB-60 |
| class I PHA synthase | - |
Pseudomonas sp. UMAB-08 |
| class I PHA synthase | - |
Pseudomonas sp. UMAB-40 |
| Class I PhaC | - |
Janthinobacterium sp. UMAB-56 |
| Class I PhaC | - |
Janthinobacterium sp. UMAB-60 |
| Class I PhaC | - |
Pseudomonas sp. UMAB-08 |
| Class I PhaC | - |
Pseudomonas sp. UMAB-40 |
| class II PHA synthase | - |
Pseudomonas sp. UMAB-08 |
| class II PHA synthase | - |
Pseudomonas sp. UMAB-40 |
| PHA synthase | - |
Janthinobacterium sp. UMAB-56 |
| PHA synthase | - |
Janthinobacterium sp. UMAB-60 |
| PHA synthase | - |
Pseudomonas sp. UMAB-08 |
| PHA synthase | - |
Pseudomonas sp. UMAB-40 |
| PHA synthase | - |
Janthinobacterium sp. UMAB-58 |
| PhaC | - |
Janthinobacterium sp. UMAB-56 |
| PhaC | - |
Janthinobacterium sp. UMAB-60 |
| PhaC | - |
Pseudomonas sp. UMAB-08 |
| PhaC | - |
Pseudomonas sp. UMAB-40 |
| PhaC | - |
Janthinobacterium sp. UMAB-58 |
| polyhydroxyalkanoate (PHA) synthase | - |
Pseudomonas sp. UMAB-08 |
| polyhydroxyalkanoate (PHA) synthase | - |
Pseudomonas sp. UMAB-40 |
| polyhydroxyalkanoate synthase | - |
Janthinobacterium sp. UMAB-56 |
| polyhydroxyalkanoate synthase | - |
Janthinobacterium sp. UMAB-60 |
| polyhydroxyalkanoate synthase | - |
Pseudomonas sp. UMAB-08 |
| polyhydroxyalkanoate synthase | - |
Pseudomonas sp. UMAB-40 |
| polyhydroxyalkanoate synthase | - |
Janthinobacterium sp. UMAB-58 |
Temperature Optimum [°C]
| Temperature Optimum [°C] | Temperature Optimum Maximum [°C] | Comment | Organism |
|---|---|---|---|
| 20 | - |
assay at | Janthinobacterium sp. UMAB-56 |
| 20 | - |
assay at | Janthinobacterium sp. UMAB-60 |
| 20 | - |
assay at | Pseudomonas sp. UMAB-08 |
| 20 | - |
assay at | Pseudomonas sp. UMAB-40 |
pH Optimum
| pH Optimum Minimum | pH Optimum Maximum | Comment | Organism |
|---|---|---|---|
| 7.8 | - |
assay at | Janthinobacterium sp. UMAB-56 |
| 7.8 | - |
assay at | Janthinobacterium sp. UMAB-60 |
| 7.8 | - |
assay at | Pseudomonas sp. UMAB-08 |
| 7.8 | - |
assay at | Pseudomonas sp. UMAB-40 |
General Information
| General Information | Comment | Organism |
|---|---|---|
| evolution | Pseudomonas isolates are found to carry PHA synthase genes which fall into two different PHA gene clusters, namely Class I and Class II, which are involved in the biosynthesis of short-chain-length-PHA (SCL-PHA) and medium-chain-length-PHA (MCL-PHA), respectively | Pseudomonas sp. UMAB-08 |
| evolution | Pseudomonas isolates are found to carry PHA synthase genes which fall into two different PHA gene clusters, namely Class I and Class II, which are involved in the biosynthesis of short-chain-length-PHA (SCL-PHA) and medium-chain-length-PHA (MCL-PHA), respectively | Pseudomonas sp. UMAB-40 |
| evolution | the Janthinobacterium isolates carry a Class I and an uncharacterized putative PHA synthase genes. No other gene involved in PHA synthesis is detected in close proximity to the uncharacterized putative PHA synthase gene in the Janthinobacterium isolates, therefore it falls into a separate clade from the ordinary Class I, II, III and IV clades of PHA synthase (PhaC) phylogenetic tree. Both of the antarctic Janthinobacterium isolates (UMAB-56 and UMAB-60) have a similar Class I PHA gene cluster as the Jantinobactarium spp. SCL-PHA producers | Janthinobacterium sp. UMAB-56 |
| evolution | the Janthinobacterium isolates carry a Class I and an uncharacterized putative PHA synthase genes. No other gene involved in PHA synthesis is detected in close proximity to the uncharacterized putative PHA synthase gene in the Janthinobacterium isolates, therefore it falls into a separate clade from the ordinary Class I, II, III and IV clades of PHA synthase (PhaC) phylogenetic tree. Both of the antarctic Janthinobacterium isolates (UMAB-56 and UMAB-60) have a similar Class I PHA gene cluster as the Jantinobactarium spp. SCL-PHA producers | Janthinobacterium sp. UMAB-60 |
| evolution | the Janthinobacterium isolates carry a Class I and an uncharacterized putative PHA synthase genes. The uncharacterized putative PHA synthase gene in the Janthinobacterium isolates falls into a separate clade from the ordinary Class I, II, III and IV clades of PHA synthase (PhaC) phylogenetic tree. Multiple sequence alignment shows that the uncharacterized putative PHA synthase gene contains all the highly conserved amino acid residues and the proposed catalytic triad of PHA synthase. Proposal of the uncharacterized PHA synthase as the new Class V PhaC | Janthinobacterium sp. UMAB-60 |
| evolution | the Janthinobacterium isolates carry a Class I and an uncharacterized putative PHA synthase genes. The uncharacterized putative PHA synthase gene in the Janthinobacterium isolates falls into a separate clade from the ordinary Class I, II, III and IV clades of PHA synthase (PhaC) phylogenetic tree. Multiple sequence alignment shows that the uncharacterized putative PHA synthase gene contains all the highly conserved amino acid residues and the proposed catalytic triad of PHA synthase. Proposal of the uncharacterized PHA synthase as the new Class V PhaC | Janthinobacterium sp. UMAB-58 |
| physiological function | Class I PHA synthases are involved in the biosynthesis of short-chain-length-polyhydroxyalkanoates (SCL-PHA) | Janthinobacterium sp. UMAB-56 |
| physiological function | Class I PHA synthases are involved in the biosynthesis of short-chain-length-polyhydroxyalkanoates (SCL-PHA) | Pseudomonas sp. UMAB-08 |
| physiological function | Class I PHA synthases are involved in the biosynthesis of short-chain-length-polyhydroxyalkanoates (SCL-PHA). The ability of UMAB-40 to produce SCL-MCL-PHA copolymers is likely due to the presence of both Class I and II PHA synthases in its genome | Pseudomonas sp. UMAB-40 |
| physiological function | Class I PHA synthases are involved in the biosynthesis of short-chain-length-polyhydroxyalkanoates (SCL-PHA). The PHA produced by UMAB-60 is a homopolymer containing C4 repeating units | Janthinobacterium sp. UMAB-60 |
| physiological function | Class II PHA synthases are involved in the biosynthesis of medium-chain-length-polyhydroxyalkanoates (MCL-PHA). Pseudomonas sp. UMAB-08 PHA gene cluster is very well conserved among the MCL-PHA producers | Pseudomonas sp. UMAB-08 |
| physiological function | Class II PHA synthases are involved in the biosynthesis of medium-chain-length-polyhydroxyalkanoates (MCL-PHA). Pseudomonas sp. UMAB-08 PHA gene cluster is very well conserved among the MCL-PHA producers. Although UMAB-40 does not produce any homopolymer (PHA having only one type of monomeric unit), small peaks of the C4 position [3-hydroxybutyrate (3HB) monomer] in addition to larger peaks at C6 to C14 are detected. The ability of UMAB-40 to produce SCL-MCL-PHA copolymers is likely due to the presence of both Class I and II PHA synthases in its genome | Pseudomonas sp. UMAB-40 |
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